生物
等位基因
基因
遗传学
驯化
基因组
数量性状位点
基因座(遗传学)
作者
Lei Gao,Itay Gonda,Honghe Sun,Qiyue Ma,Kan Bao,Denise M. Tieman,Elizabeth A. Burzynski-Chang,Tara Fish,Kaitlin A. Stromberg,Gavin L. Sacks,Theodore W. Thannhauser,Majid R. Foolad,María José Díez,José Blanca,Joaquı́n Cañizares,Yimin Xu,Esther van der Knaap,Sanwen Huang,Harry J. Klee,James J. Giovannoni,Zhangjun Fei
出处
期刊:Nature Genetics
[Springer Nature]
日期:2019-05-13
卷期号:51 (6): 1044-1051
被引量:498
标识
DOI:10.1038/s41588-019-0410-2
摘要
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding.
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